Class Journal Week 8 - Revision history

https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?action=history&feed=atom&title=Class_Journal_Week_8 Class Journal Week 8 - Revision history 2026-04-07T05:55:48Z Revision history for this page on the wiki MediaWiki 1.20.3 https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Class_Journal_Week_8&diff=4002&oldid=prev Vkuehn at 07:01, 24 October 2013 2013-10-24T07:01:06Z

<p></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 07:01, 24 October 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 142:</td> <td colspan="2" class="diff-lineno">Line 142:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[User:Gleis|Gleis]] ([[User talk:Gleis|talk]]) 16:43, 20 October 2013 (PDT)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[User:Gleis|Gleis]] ([[User talk:Gleis|talk]]) 16:43, 20 October 2013 (PDT)</div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">==[[User:Vkuehn|Viktoria Kuehn]]==</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#What were the main issues with the data and analysis identified by Baggerly and Coombs? What best practices enumerated by DataONE were violated? Which of these did Dr. Baggerly claim were common issues?</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#:The main issues with the article were the ambiguity of the procedure which made it difficult to reproduce the data and to check the accuracy by retracing the analysis. There was a lack of quality control in the data which led to a few problems with the entry of the data. For example, the data was mislabeled and off by one, and in other instances it was unclear where the resulting statistical values came from. These are common issues that occur in articles submitted to scientific journals. The quality is often checked, but the actual methods that produced the analysis is not reproduced in detail to check for correctness. </ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#What recommendations does Dr. Baggerly recommend for reproducible research? How do these correspond to what DataONE recommends?</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#:Dr. Baggerly recommends that the data behind research is easily accessible, and that the procedure is described in detail so that someone can easily check the validity of the information given by following the steps that were originally taken. He also suggests describing the program used for analysis so that the analysis can be reproduced. This would lead to more quality assurance, because it would make it easier for an outsider to reproduce the steps, which would result in more careful steps in the original so that mistakes do not surface when the information is already published. DataONE also stresses the importance of clarity in papers when conducting research. </ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#Do you have any further reaction to this case after viewing Dr. Baggerly's talk?</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#: I was shocked at the amount of error and the many ambiguities that were encountered when this research was being reproduced. I assumed that the papers published in such journals went through much more quality control before being published, especially those that were being applied to clinical trials and affecting people's lives. I was also surprised at the way many people responded when Dr. Baggerly and his team were trying to access information and notifying the journal that there were mistakes. I thought that they would have addressed this issue more openly and been more adamant about resolving the errors rather than denying them. </ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#Look at the methods and results described in the Merrell et al. (2002) paper. Do you think there is sufficient information there to reproduce their data analysis? Why or why not?</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#: It looks to me as though the methods were explained clearly, and the steps in conducting the experiment seem reproducible. SInce I am not an expert in the subject it is hard for me to be certain, the steps statistical analysis of the actual data seems to be a little sparse in detail and I do not think I would be able to reproduce this with the given information. There is a good chance, however that someone more knowledgable in the area would be able to do it with the information given.</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Journal Entry]] [[Category:Shared]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Journal Entry]] [[Category:Shared]]</div></td></tr> </table>

Vkuehn https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Class_Journal_Week_8&diff=3773&oldid=prev Gleis: addition of categories to page 2013-10-20T23:44:58Z

<p>addition of categories to page</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 23:44, 20 October 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 142:</td> <td colspan="2" class="diff-lineno">Line 142:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[User:Gleis|Gleis]] ([[User talk:Gleis|talk]]) 16:43, 20 October 2013 (PDT)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[User:Gleis|Gleis]] ([[User talk:Gleis|talk]]) 16:43, 20 October 2013 (PDT)</div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[Category:Journal Entry]] [[Category:Shared]]</ins></div></td></tr> </table>

Gleis https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Class_Journal_Week_8&diff=3772&oldid=prev Gleis at 23:43, 20 October 2013 2013-10-20T23:43:04Z

<p></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 23:43, 20 October 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 134:</td> <td colspan="2" class="diff-lineno">Line 134:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Their methods and results are well laid out and are very detailed. There is sufficient information to reproduce their data analysis, as each step is gone over in detail and several are referenced.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Their methods and results are well laid out and are very detailed. There is sufficient information to reproduce their data analysis, as each step is gone over in detail and several are referenced.</div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">=='''[[User:Gleis|Gabriel Leis]]'''==</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#The main issues identified by Baggerly and Coombs were issues with data entry and reproducibility.  In particular, the mislabeling and incorrect entry of data was detrimental to the research.  Baggerly and Coombs noticed that the gene IDs were mislabeled which resulted in any pattern found in the data to be invalid.  The researchers also had issues with consistency in transferring data.  This resulted in the data being very hard to track and lead to difficulty analyzing the procedure used by the researchers.  The researchers violated the DataOne best practices of inconsistent entry and relationships between data sets were not well defined.  Baggerly identified that inconsistent or incorrect data entry is very common especially when working with new or complex software.</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#Baggerly suggests a precise and thorough record of all procedures performed in research.  He also suggests taking the time to ensure quality data entry and organization to prevent error.  Baggerly also recommends submitting code used to analyze to data so that errors can be identified quickly and easily.</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#I am amazed at the number of ways that data can be manipulated and how easy it can be to perform errors that can be deleterious to research.  After watching this video I have a better understanding of how hard it can be to identify error in research due to the level of complexity involved in data analysis.</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#There is plenty of detail in describing the collection of samples and methods used to produce the microarray data. This part of the experiment seems reproducible.  However, the description of methodology used to analyze the data seems sparse.  Even though all raw data is included I doubt that I could reproduce the analysis of that data.</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[User:Gleis|Gleis]] ([[User talk:Gleis|talk]]) 16:43, 20 October 2013 (PDT)</ins></div></td></tr> </table>

Gleis

1. What were the main issues with the data and analysis identified by Baggerly and Coombs? What best practices enumerated by DataONE were violated? Which of these did Dr. Baggerly claim were common issues?

1. What were the main issues with the data and analysis identified by Baggerly and Coombs? What best practices enumerated by DataONE were violated? Which of these did Dr. Baggerly claim were common issues?

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